5 papers
AquaGen: Scaling generative models to molecular dynamics precision on thousands of atoms
Emmanuel Bengio, Sanjeev Raja, Yui Tik Pang +5
We present AquaGen, the first all-atom, explicit solvent, periodic-boundary-condition-aware generative model that produces molecular configurations from the Boltzmann distribution…
MarS-FM: Generative Modeling of Molecular Dynamics via Markov State Models
Kacper KapuÅniak, Cristian Gabellini, Michael Bronstein +2
Molecular Dynamics (MD) is a powerful computational microscope for probing protein functions. However, the need for fine-grained integration and the long timescales of biomolecular…
Relaxed Equivariance via Multitask Learning
Ahmed A. Elhag, T. Konstantin Rusch, Francesco Di Giovanni +1
Incorporating equivariance as an inductive bias into deep learning architectures to take advantage of the data symmetry has been successful in multiple applications, such as chemis…
A General Graph Spectral Wavelet Convolution via Chebyshev Order Decomposition
Nian Liu, Xiaoxin He, Thomas Laurent +3
Spectral graph convolution, an important tool of data filtering on graphs, relies on two essential decisions: selecting spectral bases for signal transformation and parameterizing…
Understanding Virtual Nodes: Oversquashing and Node Heterogeneity
Joshua Southern, Francesco Di Giovanni, Michael Bronstein +1
While message passing neural networks (MPNNs) have convincing success in a range of applications, they exhibit limitations such as the oversquashing problem and their inability to…